Here we showed that the shape of a trait space can be systematized through manifold learning [1]}.
The diffusion map of bacterial capabilities reveals a wealth of ecologically salient variables that span a functional coordinate system. Some show evidence of discrete capabilities such as photosynthesis in Cyanobacteria (Fig. 1). Other strategies span a continuous space representing degrees of specialization or reliance on hosts (Fig. 2). Yet others highlight strategies for energy production or stress response, some of which differentiate closely related species (Fig. S1C) or emerged, potentially through convergent evolution or gene transfer, in different branches of the tree of life (Fig. 3B).
